NM_016203.4:c.1589A>G

Variant names:

• chr7-151560613-T-C
• rs267606977
• NM_016203.4:c.1589A>G

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_016203.4(PRKAG2):​c.1589A>G​(p.His530Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PRKAG2 NM_016203.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 7.81

Genes affected

PRKAG2 (HGNC:9386): (protein kinase AMP-activated non-catalytic subunit gamma 2) AMP-activated protein kinase (AMPK) is a heterotrimeric protein composed of a catalytic alpha subunit, a noncatalytic beta subunit, and a noncatalytic regulatory gamma subunit. Various forms of each of these subunits exist, encoded by different genes. AMPK is an important energy-sensing enzyme that monitors cellular energy status and functions by inactivating key enzymes involved in regulating de novo biosynthesis of fatty acid and cholesterol. This gene is a member of the AMPK gamma subunit family. Mutations in this gene have been associated with Wolff-Parkinson-White syndrome, familial hypertrophic cardiomyopathy, and glycogen storage disease of the heart. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a binding_site (size 0) in uniprot entity AAKG2_HUMAN
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.968
• PP5: Variant 7-151560613-T-C is Pathogenic according to our data. Variant chr7-151560613-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 6854.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKAG2	NM_016203.4	c.1589A>G	p.His530Arg	missense_variant	Exon 15 of 16	ENST00000287878.9	NP_057287.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKAG2	ENST00000287878.9	c.1589A>G	p.His530Arg	missense_variant	Exon 15 of 16	1	NM_016203.4	ENSP00000287878.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy 6 Pathogenic:2

Nov 16, 2023

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is not observed in the gnomAD v2.1.1 dataset. Predicted Consequence/Location: Missense changes are a common disease-causing mechanism. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 27573176). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.90 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.91 (>=0.6, sensitivity 0.72 and precision 0.9)]. Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000006854 /PMID: 18403758). A different missense change at the same codon (p.His530Asp) has been reported to be associated with PRKAG2 related disorder (ClinVar ID: VCV000855977). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -

May 01, 2008

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided Pathogenic:1

Mar 08, 2012

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

p.His530Arg (CAT>CGT:c.1598 A>G in exon 15 of the PRKAG2 gene (NM_016203.3) The His530Arg mutation in the PRKAG2 gene has been reported previously in one individual with childhood-onset HCM, and this mutation was absent from >1,000 control alleles. In addition, the NHLBI ESP Exome Variant Server reports His530Arg was not observed in approximately 5,000 samples from individuals of European and African American backgrounds, indicating it is not a common benign variant in these populations. Although His530Arg results in a conservative substitution of one positively charged amino acid for another, the His530 residue is conserved across species. Mutations in a neighboring codon (Arg531Gln, Arg531Gly) have also been reported in association with PRKAG2-related phenotypes, supporting the functional importance of this region of the protein. In summary, the presence of His530Arg in the PRKAG2 gene is consistent with a diagnosis of a PRKAG2-related cardiomyopathy and/or Wolff-Parkinson-White (WPW) syndrome. The variant is found in HCM panel(s). -

Hypertrophic cardiomyopathy Pathogenic:1

Feb 07, 2018

Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype Pathogenic:1

Oct 11, 2021

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.H530R pathogenic mutation (also known as c.1589A>G), located in coding exon 15 of the PRKAG2 gene, results from an A to G substitution at nucleotide position 1589. The histidine at codon 530 is replaced by arginine, an amino acid with highly similar properties. This variant has been reported in individuals with hypertrophic cardiomyopathy (HCM), Wolff-Parkinson-White syndrome, and other cardiac arrhythmias, and it has been shown to segregate with disease in affected family members (Morita H et al. N Engl J Med, 2008 May;358:1899-908; Epicoco G et al. JACC Clin Electrophysiol, 2018 10;4:1377-1378; Aggarwal V et al. Ann Pediatr Cardiol;8:153-6; Xie C et al. Cell Res, 2016 Oct;26:1099-1111; Thevenon J et al. Europace, 2017 Apr;19:651-659; Lu C et al. J Transl Med, 2018 08;16:241). Functional studies in transgenic mouse models demonstrated consistent PRKAG2-related cardiac findings, including significant glycogen accumulation (Xie C et al. Cell Res, 2016 Oct;26:1099-1111). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Lethal congenital glycogen storage disease of heart Pathogenic:1

Apr 17, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 530 of the PRKAG2 protein (p.His530Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with PRKAG2-related cardiac conditions, including hypertrophic cardiomyopathy and Wolff-Parkinson-White syndrome (PMID: 18403758, 26085771, 28431061; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 6854). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PRKAG2 protein function. Experimental studies have shown that this missense change affects PRKAG2 function (PMID: 27573176). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
CardioboostCm	Uncertain	0.88
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.45
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.80	D;.;.;.
Eigen	Uncertain	0.68
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	D;D;D;D
M_CAP	Uncertain	0.14	D
MetaRNN	Pathogenic	0.97	D;D;D;D
MetaSVM	Uncertain	0.75	D
MutationAssessor	Uncertain	2.8	M;.;.;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Pathogenic	-7.4	D;D;D;D
REVEL	Pathogenic	0.90
Sift	Uncertain	0.013	D;D;D;D
Sift4G	Pathogenic	0.0	D;T;D;D
Polyphen		0.89	P;.;.;.
Vest4		0.97
MutPred		0.88		Gain of MoRF binding (P = 0.0425);.;.;.;
MVP		0.98
MPC		1.8
ClinPred		0.99	D
GERP RS		5.8
Varity_R		0.84
gMVP		0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs267606977; hg19: chr7-151257699;